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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-01-04, 17:12 based on data in: /scratch/lspencer/snowcrab-OA-2022/fastqc/raw


        General Statistics

        Showing 252/252 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        5010_10_S10_L003_R1_001
        76.5%
        51%
        55.4
        5010_10_S10_L003_R2_001
        73.2%
        50%
        55.4
        5010_11_S11_L003_R1_001
        75.9%
        50%
        51.6
        5010_11_S11_L003_R2_001
        72.8%
        50%
        51.6
        5010_12_S12_L003_R1_001
        77.2%
        52%
        49.7
        5010_12_S12_L003_R2_001
        73.0%
        51%
        49.7
        5010_13_S13_L003_R1_001
        77.3%
        52%
        52.0
        5010_13_S13_L003_R2_001
        73.1%
        51%
        52.0
        5010_14_S14_L003_R1_001
        78.3%
        52%
        61.7
        5010_14_S14_L003_R2_001
        74.3%
        51%
        61.7
        5010_15_S15_L003_R1_001
        76.8%
        51%
        51.0
        5010_15_S15_L003_R2_001
        72.2%
        50%
        51.0
        5010_16_S16_L003_R1_001
        76.7%
        51%
        50.3
        5010_16_S16_L003_R2_001
        72.1%
        50%
        50.3
        5010_17_S17_L003_R1_001
        75.5%
        51%
        53.0
        5010_17_S17_L003_R2_001
        71.2%
        51%
        53.0
        5010_18_S18_L003_R1_001
        76.1%
        52%
        45.9
        5010_18_S18_L003_R2_001
        72.0%
        51%
        45.9
        5010_19_S19_L003_R1_001
        77.4%
        52%
        41.1
        5010_19_S19_L003_R2_001
        72.7%
        51%
        41.1
        5010_1_S1_L003_R1_001
        78.2%
        52%
        44.9
        5010_1_S1_L003_R2_001
        73.6%
        51%
        44.9
        5010_20_S20_L003_R1_001
        75.1%
        52%
        42.6
        5010_20_S20_L003_R2_001
        70.7%
        51%
        42.6
        5010_21_S21_L003_R1_001
        73.7%
        51%
        42.8
        5010_21_S21_L003_R2_001
        69.3%
        51%
        42.8
        5010_22_S22_L003_R1_001
        75.3%
        51%
        42.6
        5010_22_S22_L003_R2_001
        71.1%
        51%
        42.6
        5010_23_S23_L003_R1_001
        75.5%
        52%
        41.6
        5010_23_S23_L003_R2_001
        70.6%
        51%
        41.6
        5010_24_S24_L003_R1_001
        75.4%
        51%
        47.9
        5010_24_S24_L003_R2_001
        70.4%
        51%
        47.9
        5010_25_S25_L003_R1_001
        76.5%
        52%
        48.2
        5010_25_S25_L003_R2_001
        71.9%
        51%
        48.2
        5010_26_S26_L003_R1_001
        73.7%
        51%
        46.5
        5010_26_S26_L003_R2_001
        68.7%
        50%
        46.5
        5010_27_S27_L003_R1_001
        76.5%
        52%
        47.4
        5010_27_S27_L003_R2_001
        71.1%
        51%
        47.4
        5010_28_S28_L003_R1_001
        75.8%
        52%
        41.0
        5010_28_S28_L003_R2_001
        71.3%
        51%
        41.0
        5010_29_S29_L003_R1_001
        75.9%
        51%
        42.9
        5010_29_S29_L003_R2_001
        70.7%
        50%
        42.9
        5010_2_S2_L003_R1_001
        75.0%
        52%
        44.9
        5010_2_S2_L003_R2_001
        70.6%
        51%
        44.9
        5010_30_S30_L003_R1_001
        78.7%
        52%
        43.5
        5010_30_S30_L003_R2_001
        74.6%
        50%
        43.5
        5010_31_S31_L003_R1_001
        75.8%
        52%
        46.4
        5010_31_S31_L003_R2_001
        71.0%
        52%
        46.4
        5010_32_S32_L003_R1_001
        75.2%
        51%
        46.3
        5010_32_S32_L003_R2_001
        71.4%
        50%
        46.3
        5010_33_S33_L003_R1_001
        78.5%
        51%
        47.6
        5010_33_S33_L003_R2_001
        74.1%
        50%
        47.6
        5010_34_S34_L003_R1_001
        77.7%
        51%
        45.3
        5010_34_S34_L003_R2_001
        73.2%
        50%
        45.3
        5010_35_S35_L003_R1_001
        76.9%
        51%
        47.4
        5010_35_S35_L003_R2_001
        72.7%
        50%
        47.4
        5010_36_S36_L003_R1_001
        78.8%
        51%
        41.9
        5010_36_S36_L003_R2_001
        76.9%
        50%
        41.9
        5010_37_S37_L003_R1_001
        75.2%
        51%
        40.9
        5010_37_S37_L003_R2_001
        70.1%
        50%
        40.9
        5010_38_S38_L003_R1_001
        75.1%
        51%
        44.7
        5010_38_S38_L003_R2_001
        71.0%
        50%
        44.7
        5010_39_S39_L003_R1_001
        77.2%
        52%
        45.6
        5010_39_S39_L003_R2_001
        72.7%
        51%
        45.6
        5010_3_S3_L003_R1_001
        75.8%
        52%
        46.2
        5010_3_S3_L003_R2_001
        71.1%
        51%
        46.2
        5010_40_S40_L003_R1_001
        76.7%
        52%
        50.0
        5010_40_S40_L003_R2_001
        72.2%
        51%
        50.0
        5010_41_S41_L003_R1_001
        75.8%
        52%
        46.7
        5010_41_S41_L003_R2_001
        71.6%
        51%
        46.7
        5010_42_S42_L003_R1_001
        76.9%
        52%
        50.4
        5010_42_S42_L003_R2_001
        72.6%
        51%
        50.4
        5010_43_S43_L003_R1_001
        74.6%
        51%
        40.3
        5010_43_S43_L003_R2_001
        69.8%
        50%
        40.3
        5010_44_S44_L003_R1_001
        80.8%
        51%
        80.2
        5010_44_S44_L003_R2_001
        76.6%
        50%
        80.2
        5010_45_S45_L003_R1_001
        47.4%
        52%
        0.9
        5010_45_S45_L003_R2_001
        42.2%
        51%
        0.9
        5010_46_S46_L003_R1_001
        72.7%
        50%
        42.5
        5010_46_S46_L003_R2_001
        68.4%
        50%
        42.5
        5010_47_S47_L003_R1_001
        75.8%
        51%
        49.7
        5010_47_S47_L003_R2_001
        72.6%
        51%
        49.7
        5010_48_S48_L003_R1_001
        75.3%
        52%
        43.0
        5010_48_S48_L003_R2_001
        70.3%
        51%
        43.0
        5010_49_S49_L003_R1_001
        76.1%
        52%
        48.3
        5010_49_S49_L003_R2_001
        72.4%
        51%
        48.3
        5010_4_S4_L003_R1_001
        77.8%
        51%
        41.3
        5010_4_S4_L003_R2_001
        73.8%
        51%
        41.3
        5010_50_S50_L003_R1_001
        76.9%
        51%
        48.7
        5010_50_S50_L003_R2_001
        72.8%
        51%
        48.7
        5010_51_S51_L003_R1_001
        78.1%
        51%
        54.5
        5010_51_S51_L003_R2_001
        74.8%
        50%
        54.5
        5010_52_S52_L003_R1_001
        74.5%
        51%
        47.5
        5010_52_S52_L003_R2_001
        71.1%
        50%
        47.5
        5010_53_S53_L003_R1_001
        78.5%
        52%
        67.6
        5010_53_S53_L003_R2_001
        74.6%
        51%
        67.6
        5010_54_S54_L003_R1_001
        77.9%
        51%
        66.2
        5010_54_S54_L003_R2_001
        74.4%
        50%
        66.2
        5010_55_S55_L003_R1_001
        76.7%
        52%
        50.6
        5010_55_S55_L003_R2_001
        72.6%
        51%
        50.6
        5010_56_S56_L003_R1_001
        77.5%
        51%
        59.3
        5010_56_S56_L003_R2_001
        74.6%
        50%
        59.3
        5010_57_S57_L003_R1_001
        76.4%
        51%
        47.3
        5010_57_S57_L003_R2_001
        72.8%
        51%
        47.3
        5010_58_S58_L003_R1_001
        75.0%
        51%
        47.5
        5010_58_S58_L003_R2_001
        71.5%
        51%
        47.5
        5010_59_S59_L003_R1_001
        76.8%
        52%
        49.4
        5010_59_S59_L003_R2_001
        72.9%
        51%
        49.4
        5010_5_S5_L003_R1_001
        75.0%
        51%
        37.9
        5010_5_S5_L003_R2_001
        70.8%
        51%
        37.9
        5010_60_S60_L003_R1_001
        79.6%
        51%
        56.8
        5010_60_S60_L003_R2_001
        76.0%
        50%
        56.8
        5010_61_S61_L003_R1_001
        78.6%
        51%
        68.4
        5010_61_S61_L003_R2_001
        74.8%
        50%
        68.4
        5010_62_S62_L003_R1_001
        81.7%
        52%
        86.7
        5010_62_S62_L003_R2_001
        77.9%
        51%
        86.7
        5010_63_S63_L003_R1_001
        76.3%
        51%
        49.1
        5010_63_S63_L003_R2_001
        72.9%
        51%
        49.1
        5010_6_S6_L003_R1_001
        74.9%
        52%
        35.4
        5010_6_S6_L003_R2_001
        70.6%
        51%
        35.4
        5010_7_S7_L003_R1_001
        77.2%
        53%
        36.2
        5010_7_S7_L003_R2_001
        73.1%
        52%
        36.2
        5010_8_S8_L003_R1_001
        74.5%
        52%
        47.3
        5010_8_S8_L003_R2_001
        70.8%
        51%
        47.3
        5010_9_S9_L003_R1_001
        75.8%
        51%
        54.3
        5010_9_S9_L003_R2_001
        71.5%
        50%
        54.3
        5329_10_S73_L004_R1_001
        76.8%
        51%
        55.3
        5329_10_S73_L004_R2_001
        73.7%
        50%
        55.3
        5329_11_S74_L004_R1_001
        76.6%
        50%
        53.8
        5329_11_S74_L004_R2_001
        74.0%
        49%
        53.8
        5329_12_S75_L004_R1_001
        77.4%
        52%
        49.9
        5329_12_S75_L004_R2_001
        73.5%
        51%
        49.9
        5329_13_S76_L004_R1_001
        77.8%
        52%
        52.1
        5329_13_S76_L004_R2_001
        73.5%
        51%
        52.1
        5329_14_S77_L004_R1_001
        78.7%
        52%
        62.0
        5329_14_S77_L004_R2_001
        75.0%
        51%
        62.0
        5329_15_S78_L004_R1_001
        77.0%
        51%
        50.5
        5329_15_S78_L004_R2_001
        72.7%
        50%
        50.5
        5329_16_S79_L004_R1_001
        77.2%
        51%
        50.0
        5329_16_S79_L004_R2_001
        72.9%
        50%
        50.0
        5329_17_S80_L004_R1_001
        76.1%
        51%
        53.5
        5329_17_S80_L004_R2_001
        71.9%
        51%
        53.5
        5329_18_S81_L004_R1_001
        76.7%
        52%
        46.7
        5329_18_S81_L004_R2_001
        72.3%
        51%
        46.7
        5329_19_S82_L004_R1_001
        77.8%
        52%
        41.5
        5329_19_S82_L004_R2_001
        73.2%
        51%
        41.5
        5329_1_S64_L004_R1_001
        78.6%
        52%
        45.5
        5329_1_S64_L004_R2_001
        74.2%
        51%
        45.5
        5329_20_S83_L004_R1_001
        75.4%
        52%
        42.7
        5329_20_S83_L004_R2_001
        71.2%
        51%
        42.7
        5329_21_S84_L004_R1_001
        74.2%
        51%
        43.7
        5329_21_S84_L004_R2_001
        69.8%
        51%
        43.7
        5329_22_S85_L004_R1_001
        75.6%
        51%
        42.6
        5329_22_S85_L004_R2_001
        71.5%
        50%
        42.6
        5329_23_S86_L004_R1_001
        76.0%
        52%
        42.6
        5329_23_S86_L004_R2_001
        71.8%
        51%
        42.6
        5329_24_S87_L004_R1_001
        75.8%
        51%
        48.2
        5329_24_S87_L004_R2_001
        71.1%
        51%
        48.2
        5329_25_S88_L004_R1_001
        77.3%
        52%
        49.2
        5329_25_S88_L004_R2_001
        72.8%
        50%
        49.2
        5329_26_S89_L004_R1_001
        74.4%
        51%
        48.1
        5329_26_S89_L004_R2_001
        69.8%
        50%
        48.1
        5329_27_S90_L004_R1_001
        76.8%
        52%
        47.9
        5329_27_S90_L004_R2_001
        71.8%
        51%
        47.9
        5329_28_S91_L004_R1_001
        76.2%
        52%
        41.2
        5329_28_S91_L004_R2_001
        71.8%
        51%
        41.2
        5329_29_S92_L004_R1_001
        76.4%
        51%
        43.9
        5329_29_S92_L004_R2_001
        71.6%
        50%
        43.9
        5329_2_S65_L004_R1_001
        75.6%
        52%
        45.8
        5329_2_S65_L004_R2_001
        71.3%
        51%
        45.8
        5329_30_S93_L004_R1_001
        79.4%
        52%
        44.5
        5329_30_S93_L004_R2_001
        75.6%
        50%
        44.5
        5329_31_S94_L004_R1_001
        76.3%
        52%
        47.4
        5329_31_S94_L004_R2_001
        71.7%
        52%
        47.4
        5329_32_S95_L004_R1_001
        75.9%
        51%
        48.8
        5329_32_S95_L004_R2_001
        72.5%
        50%
        48.8
        5329_33_S96_L004_R1_001
        78.9%
        51%
        47.5
        5329_33_S96_L004_R2_001
        74.6%
        50%
        47.5
        5329_34_S97_L004_R1_001
        78.2%
        51%
        45.8
        5329_34_S97_L004_R2_001
        73.9%
        50%
        45.8
        5329_35_S98_L004_R1_001
        77.6%
        51%
        48.5
        5329_35_S98_L004_R2_001
        73.4%
        50%
        48.5
        5329_36_S99_L004_R1_001
        79.4%
        51%
        42.8
        5329_36_S99_L004_R2_001
        77.7%
        50%
        42.8
        5329_37_S100_L004_R1_001
        75.5%
        51%
        41.5
        5329_37_S100_L004_R2_001
        70.6%
        50%
        41.5
        5329_38_S101_L004_R1_001
        75.9%
        51%
        46.0
        5329_38_S101_L004_R2_001
        72.0%
        50%
        46.0
        5329_39_S102_L004_R1_001
        77.6%
        52%
        47.5
        5329_39_S102_L004_R2_001
        73.4%
        51%
        47.5
        5329_3_S66_L004_R1_001
        76.4%
        52%
        47.4
        5329_3_S66_L004_R2_001
        72.0%
        51%
        47.4
        5329_40_S103_L004_R1_001
        77.4%
        52%
        51.2
        5329_40_S103_L004_R2_001
        72.8%
        51%
        51.2
        5329_41_S104_L004_R1_001
        76.3%
        52%
        47.5
        5329_41_S104_L004_R2_001
        72.4%
        51%
        47.5
        5329_42_S105_L004_R1_001
        77.5%
        52%
        51.7
        5329_42_S105_L004_R2_001
        73.3%
        51%
        51.7
        5329_43_S106_L004_R1_001
        75.2%
        51%
        41.0
        5329_43_S106_L004_R2_001
        70.6%
        50%
        41.0
        5329_44_S107_L004_R1_001
        81.2%
        51%
        80.6
        5329_44_S107_L004_R2_001
        77.0%
        50%
        80.6
        5329_45_S108_L004_R1_001
        48.3%
        52%
        0.9
        5329_45_S108_L004_R2_001
        43.2%
        51%
        0.9
        5329_46_S109_L004_R1_001
        73.2%
        50%
        43.2
        5329_46_S109_L004_R2_001
        69.0%
        50%
        43.2
        5329_47_S110_L004_R1_001
        76.2%
        51%
        50.6
        5329_47_S110_L004_R2_001
        73.3%
        51%
        50.6
        5329_48_S111_L004_R1_001
        76.1%
        52%
        44.6
        5329_48_S111_L004_R2_001
        71.4%
        51%
        44.6
        5329_49_S112_L004_R1_001
        76.4%
        52%
        48.7
        5329_49_S112_L004_R2_001
        72.9%
        51%
        48.7
        5329_4_S67_L004_R1_001
        78.6%
        51%
        43.2
        5329_4_S67_L004_R2_001
        74.7%
        50%
        43.2
        5329_50_S113_L004_R1_001
        77.6%
        51%
        51.0
        5329_50_S113_L004_R2_001
        73.7%
        51%
        51.0
        5329_51_S114_L004_R1_001
        78.5%
        51%
        54.8
        5329_51_S114_L004_R2_001
        75.2%
        50%
        54.8
        5329_52_S115_L004_R1_001
        75.3%
        51%
        48.2
        5329_52_S115_L004_R2_001
        72.1%
        50%
        48.2
        5329_53_S116_L004_R1_001
        79.0%
        52%
        68.7
        5329_53_S116_L004_R2_001
        75.2%
        51%
        68.7
        5329_54_S117_L004_R1_001
        78.2%
        51%
        66.6
        5329_54_S117_L004_R2_001
        74.7%
        50%
        66.6
        5329_55_S118_L004_R1_001
        77.1%
        52%
        51.4
        5329_55_S118_L004_R2_001
        73.3%
        51%
        51.4
        5329_56_S119_L004_R1_001
        78.0%
        51%
        59.3
        5329_56_S119_L004_R2_001
        75.0%
        50%
        59.3
        5329_57_S120_L004_R1_001
        76.8%
        51%
        47.9
        5329_57_S120_L004_R2_001
        73.5%
        51%
        47.9
        5329_58_S121_L004_R1_001
        75.5%
        51%
        48.7
        5329_58_S121_L004_R2_001
        72.4%
        51%
        48.7
        5329_59_S122_L004_R1_001
        77.3%
        52%
        50.3
        5329_59_S122_L004_R2_001
        73.5%
        51%
        50.3
        5329_5_S68_L004_R1_001
        75.8%
        51%
        39.2
        5329_5_S68_L004_R2_001
        71.8%
        51%
        39.2
        5329_60_S123_L004_R1_001
        80.2%
        51%
        58.7
        5329_60_S123_L004_R2_001
        76.9%
        50%
        58.7
        5329_61_S124_L004_R1_001
        79.3%
        51%
        70.5
        5329_61_S124_L004_R2_001
        75.6%
        50%
        70.5
        5329_62_S125_L004_R1_001
        82.1%
        52%
        87.6
        5329_62_S125_L004_R2_001
        78.5%
        51%
        87.6
        5329_63_S126_L004_R1_001
        76.6%
        51%
        49.2
        5329_63_S126_L004_R2_001
        73.3%
        51%
        49.2
        5329_6_S69_L004_R1_001
        75.7%
        52%
        36.5
        5329_6_S69_L004_R2_001
        71.5%
        51%
        36.5
        5329_7_S70_L004_R1_001
        77.7%
        53%
        36.4
        5329_7_S70_L004_R2_001
        73.7%
        52%
        36.4
        5329_8_S71_L004_R1_001
        75.1%
        52%
        48.6
        5329_8_S71_L004_R2_001
        71.5%
        51%
        48.6
        5329_9_S72_L004_R1_001
        76.1%
        51%
        53.9
        5329_9_S72_L004_R2_001
        71.9%
        50%
        53.9

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (157bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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